Figures and data
The comparison of SNR between implanted single loop (IL) and implanted figure 8 (IF8) RF coils and the commercial phase-array surface coil.
A. The representative picture of the implantable single-loop RF coil. B. The representative picture of the figure 8 RF coil. C. The bar graph shows the SNR of anatomical images acquired with different RF coils using the 9.4T scanner 
High resolution awake mouse fMRI at 14T.
A. The awake mouse setup with head-fixed position in a customer-built cradle for visual and vibrissa stimulation. B. The representative fMRI time course of an awake mouse based on raw image data acquired from high-resolution EPI, enabling the trace of motion-induced artifacts. C. The anatomical MRI images (FLASH) acquired from one representative awake mouse, showing minimal susceptibility and whole brain coverage from the implanted surface coil. D. The raw EPI fMRI image with same spatial resolution as the anatomical FLASH image. E. The snapshot of the distorted images due to motion of the awake mouse during scanning (Supplementary Movie 2 shows the video of motion-induced artifacts throughout the fMRI trial).
Visual stimulation-evoked high-resolution fMRI of awake mice.
A. The brain-wide functional maps of awake mice show the strong positive BOLD activation in the visual cortex (VC), lateral geniculate nucleus (LGN), superior colliculus (SC), and anterior cingulate area (ACA)) based on the group analysis. B. The averaged time course of the ROIs based on brain atlas, demonstrating the evoked positive BOLD signal changes upon the 8s visual stimulation (5Hz 530nm and 5.1Hz 490nm 20ms light pluses). Each graph displays the average of 162 sets of 3 stimulation epochs. Shaded regions represent standard error. Red lines represent the 8s stimulation duration. C. The functional maps overlain with the brain atlas to highlight the activated brains regions: VC, SC, LGN, and ACA.
The processing pipeline of the awake mouse fMRI datasets.
The workflow diagram is described through the following steps: raw data registration, outlier removal, volume registration-based motion file estimation, Motion removal, linear regression with the censoring function, functional map demonstration.
Vibrissa stimulation-evoked high-resolution fMRI of awake mice.
A. The brain-wide functional maps of awake mice show the strong positive BOLD activation in the contralateral barrel cortex (BC) and ventral posteromedial nucleus (VPM) and posterior thalamic nucleus (PO). Positive BOLD signals are also detected at the motor cortex (MC) and the ventral retrosplenial area (VRA), as well as at the ipsilateral BC and thalamic nuclei. B. The functional maps are overlain with the brain atlas to highlight the activated vibrissa thalamocortical pathway (VPM→BC) and the VRA in awake mice. C. The averaged time course based on the brain atlas ROIs for VMP, BC, and VRA, demonstrating positive BOLD signal changes upon the 8s air-puff vibrissa stimulation (8Hz, 10ms). Each graph displays the average of 279 sets of 3 stimulation epochs. Shaded regions represent standard error. Red lines represent the 8s stimulation duration.
The awake mouse fMRI with vibrissa stimulation.
Left panel is the average functional map highlighting BOLD activation in the contralateral BC. Right panel is a 3x3 matrix presenting the time course data from the green box located in the barrel cortex. The positive BOLD signals can be well identified through the ten epoch on/off stimulation paradigm.
VRA-based brain-wide correlation maps at different time shifts.
A. The VRA-based correlation maps at -6s and 0s time shifts of awake mice with repetitive stimulation (REP). The strong correlation in the contralateral BC is shown in the correlation map at the -6s time shift (red box). B. The VRA-based correlation maps at -6s and 0s time shifts of awake mice with randomized stimulation (RAD). No correlation is detected in the contralateral BC at the -6s time shift (red box). C. The enlarged images from the -6s time shift correlation maps of REP and RAD groups, demonstrating the strong correlation patterns located at the contralateral BC only in the REP group. D. The averaged time course from both contralateral BC and VRA of REP and RAD groups, showing that early positive BOLD signals detected at 2 s prior to the stimulation in contralateral BC of the REP group and no significance difference detected in VRA. E. The bar graph presents the mean BOLD signals of contralateral BC at 2s prior to stimulation time point and peak signals of VRA in REP and RAD groups. The inset is the expanded bar graph to show the significantly higher BOLD signals detected in the contralateral BC at 2 s prior to stimulation in REP group (p=0.015, REP graph displays the average of 930 stimulation epochs, RAD graph displays the average of 240 stimulation epochs)
